def test_bg_correction_index():
qpi, path, dout = setup_test_data(num=2)
path_out = drymass.convert(path_in=path,
dir_out=dout,
bg_data_amp=1,
bg_data_pha=1)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qps:
# background correction with same input image will result
# in a flat QPImage.
assert np.all(qps[0].pha == 0)
assert np.all(qps[0].amp == 1)
# To be absolutely sure this works, append a blank
# QPImage and do it again.
with qpimage.QPSeries(h5file=path, h5mode="a") as qps:
pha = .5 * np.ones(qps[0].shape)
amp = .9 * np.ones(qps[0].shape)
qps.add_qpimage(
qpimage.QPImage(data=(pha, amp), which_data="phase,amplitude"))
path_out = drymass.convert(path_in=path,
dir_out=dout,
bg_data_amp=3,
bg_data_pha=3)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qps:
# background correction with same input image will result
# in a flat QPImage.
assert np.allclose(qps[0].pha, qpi.pha - .5)
assert np.allclose(qps[0].amp, qpi.amp / .9)
def test_exclude_roi():
_, path_in, path_out = setup_test_data(num=2)
cli_extract_roi(path=path_in)
cfg = config.ConfigFile(path_out)
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 2
# remove first image
cfg.set_value(section="roi", key="ignore data", value="1.1")
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 1
# remove second image
cfg.set_value(section="roi", key="ignore data", value="2")
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 1
# remove all
cfg.set_value(section="roi", key="ignore data", value=["1", "2"])
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 0
def test_identifier():
h5file = pathlib.Path(__file__).parent / "data" / "bg_tilt.h5"
qpi = qpimage.QPImage(h5file=h5file, h5mode="r")
series1 = qpimage.QPSeries(qpimage_list=[qpi, qpi, qpi],
identifier="test_identifier")
assert series1.identifier == "test_identifier"
series2 = qpimage.QPSeries(qpimage_list=[qpi, qpi, qpi])
assert series2.identifier is None
def setup_test_data(radius=30,
pxsize=1e-6,
size=200,
cx=80,
cy=120,
num=1,
identifier=None,
medium_index=1.335,
wavelength=550e-9,
bg=None):
x = np.arange(size).reshape(-1, 1)
y = np.arange(size).reshape(1, -1)
r = np.sqrt((x - cx)**2 + (y - cy)**2)
image = (r < radius) * 1.3
if bg is not None:
image += bg
qpi = qpimage.QPImage(data=image,
which_data="phase",
meta_data={
"pixel size": pxsize,
"medium index": medium_index,
"wavelength": wavelength
})
path = tempfile.mktemp(suffix=".h5", prefix="drymass_test_roi")
dout = tempfile.mkdtemp(prefix="drymass_test_roi_")
with qpimage.QPSeries(h5file=path, identifier=identifier) as qps:
for ii in range(num):
qpid = "{}_test_{}".format(identifier, ii)
qps.add_qpimage(qpi, identifier=qpid)
return qpi, path, dout
def test_bg_corr_mask():
radius = 30
pxsize = 1e-6
size = 200
bg = np.zeros((size, size)) + .1
bg += np.linspace(-.3, .5, size).reshape(-1, 1)
_, path, dout = setup_test_data(radius=radius,
size=size,
pxsize=pxsize,
bg=bg)
qpiref, p2, d2 = setup_test_data(radius=radius,
size=size,
pxsize=pxsize,
bg=None)
bg_pha_kw = {
"fit_offset": "mean",
"fit_profile": "tilt",
"border_perc": 0,
"border_px": 0
}
path_out = drymass.extract_roi(path,
dir_out=dout,
size_m=2 * radius * pxsize,
bg_pha_kw=bg_pha_kw,
bg_pha_mask_radial_clearance=1.1)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qpso:
assert np.allclose(np.min(qpso[0].pha), 0, atol=4e-9, rtol=0)
assert np.allclose(np.max(qpso[0].pha),
np.max(qpiref.pha),
atol=1.1e-7,
rtol=0)
def setup_test_data(radius_px=30, size=200, pxsize=1e-6, medium_index=1.335,
wavelength=550e-9, num=1):
x = np.arange(size).reshape(-1, 1)
y = np.arange(size).reshape(1, -1)
cx = 80
cy = 120
r = np.sqrt((x - cx)**2 + (y - cy)**2)
pha = (r < radius_px) * 1.3
amp = .5 + np.roll(pha, 10) / pha.max()
qpi = qpimage.QPImage(data=(pha, amp),
which_data="phase,amplitude",
meta_data={"pixel size": pxsize,
"medium index": medium_index,
"wavelength": wavelength})
path_in = tempfile.mktemp(suffix=".h5", prefix="drymass_test_cli_sphere")
path_in = pathlib.Path(path_in)
with qpimage.QPSeries(h5file=path_in, h5mode="w", identifier="tt") as qps:
for ii in range(num):
qps.add_qpimage(qpi, identifier="image_{}".format(ii))
# add drymass configuration file
path_out = path_in.with_name(path_in.name + dialog.OUTPUT_SUFFIX)
path_out.mkdir()
cfg = config.ConfigFile(path_out)
cfg.set_value(section="meta", key="pixel size um", value=pxsize*1e6)
cfg.set_value(section="meta", key="wavelength nm", value=wavelength*1e9)
cfg.set_value(section="meta", key="medium index", value=medium_index)
cfg.set_value(section="specimen", key="size um",
value=radius_px*2*pxsize*1e6)
cfg.set_value(section="sphere", key="method", value="edge")
cfg.set_value(section="sphere", key="model", value="projection")
return qpi, path_in, path_out
def setup_test_data(radius_px=30,
size=200,
pxsize=1e-6,
medium_index=1.335,
wavelength=550e-9,
num=1):
x = np.arange(size).reshape(-1, 1)
y = np.arange(size).reshape(1, -1)
cx = 80
cy = 120
r = np.sqrt((x - cx)**2 + (y - cy)**2)
image = (r < radius_px) * 1.3
qpi = qpimage.QPImage(data=image,
which_data="phase",
meta_data={
"pixel size": pxsize,
"medium index": medium_index,
"wavelength": wavelength
})
path = tempfile.mktemp(suffix=".h5", prefix="drymass_test_sphere")
dout = tempfile.mkdtemp(prefix="drymass_test_sphere_")
identifier = "abcdef:123456:a1b2c3"
with qpimage.QPSeries(h5file=path, identifier=identifier) as qps:
for ii in range(num):
qps.add_qpimage(qpi, identifier="test_{}".format(ii))
return qpi, path, dout
def setup_test_data(radius_px=30,
size=200,
pxsize=1e-6,
medium_index=1.335,
wavelength=550e-9,
num=1):
x = np.arange(size).reshape(-1, 1)
y = np.arange(size).reshape(1, -1)
cx = 80
cy = 120
r = np.sqrt((x - cx)**2 + (y - cy)**2)
pha = (r < radius_px) * 1.3
amp = .5 + np.roll(pha, 10) / pha.max()
qpi = qpimage.QPImage(data=(pha, amp),
which_data="phase,amplitude",
meta_data={
"pixel size": pxsize,
"medium index": medium_index,
"wavelength": wavelength
})
path = tempfile.mktemp(suffix=".h5", prefix="drymass_test_convert")
dout = tempfile.mkdtemp(prefix="drymass_test_sphere_")
with qpimage.QPSeries(h5file=path, h5mode="w") as qps:
for ii in range(num):
qps.add_qpimage(qpi, identifier="test_{}".format(ii))
return qpi, path, dout
def test_bg_correction_none_bad():
_qpi, path, dout = setup_test_data(num=2)
path_out = drymass.convert(path_in=path, dir_out=dout, bg_data_amp=1)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qps:
# background correction with same input image will result
# in a flat QPImage.
assert not np.all(qps[0].pha == 0)
assert np.all(qps[0].amp == 1)
path_out = drymass.convert(path_in=path, dir_out=dout, bg_data_pha=1)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qps:
# background correction with same input image will result
# in a flat QPImage.
assert np.all(qps[0].pha == 0)
assert not np.all(qps[0].amp == 1)
def test_exclude_roi_bad():
_, path_in, path_out = setup_test_data(num=2)
cli_extract_roi(path=path_in)
cfg = config.ConfigFile(path_out)
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert len(qps) == 2
# bad image
cfg.set_value(section="roi", key="ignore data", value="3")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
# bad roi
cfg.set_value(section="roi", key="ignore data", value="1.2")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
# bad image and roi
cfg.set_value(section="roi", key="ignore data", value="4.2")
try:
cli_extract_roi(path=path_in, ret_data=True)
except ValueError:
pass
else:
assert False
def test_base():
qpi, path_in, path_out = setup_test_data(num=2)
h5data = cli_convert(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data, h5mode="r") as qps:
assert np.allclose(qpi.pha, qps[0].pha)
assert np.allclose(qpi.amp, qps[0].amp)
def test_getitem_identifier():
size = 20
pha = np.repeat(np.linspace(0, 10, size), size)
pha = pha.reshape(size, size)
qpi1 = qpimage.QPImage(data=1.1 * pha,
which_data="phase",
meta_data={"identifier": "peter"})
qpi2 = qpimage.QPImage(data=1.2 * pha,
which_data="phase",
meta_data={"identifier": "hans"})
qpi3 = qpimage.QPImage(data=1.3 * pha,
which_data="phase",
meta_data={"identifier": "doe"})
series = qpimage.QPSeries(qpimage_list=[qpi1, qpi2, qpi3])
assert "peter" in series
assert "peter_bad" not in series
assert series["peter"] == qpi1
assert series["peter"] != qpi2
assert series["hans"] == qpi2
assert series["doe"] == qpi3
try:
series["john"]
except KeyError:
pass
else:
assert False, "'john' is not in series"
try:
series.add_qpimage(qpi1)
except ValueError:
pass
else:
assert False, "Adding QPImage with same identifier should not work"
def test_getitem():
size = 20
pha = np.repeat(np.linspace(0, 10, size), size)
pha = pha.reshape(size, size)
qpi1 = qpimage.QPImage(data=1.1 * pha, which_data="phase")
qpi2 = qpimage.QPImage(data=1.2 * pha, which_data="phase")
qpi3 = qpimage.QPImage(data=1.3 * pha, which_data="phase")
series = qpimage.QPSeries(qpimage_list=[qpi1, qpi2, qpi3])
assert qpi1 != qpi2
assert qpi1 != qpi3
assert series[0] == qpi1
assert series[1] == qpi2
assert series[2] == qpi3
assert series[-3] == qpi1
assert series[-2] == qpi2
assert series[-1] == qpi3
try:
series[-4]
except ValueError:
pass
else:
assert False, "Negative index exceeds size."
def test_convert_with_profile():
cfgpath = setup_config(pxsize=1.34e-6,
medium_index=1.346,
wavelength=554.2e-9)
_, path_in, path_out = setup_test_data()
argsadd = argparse.Namespace(subparser_name="add",
name="test_8440_prof_convert",
path=cfgpath)
profile.cli_profile(args=argsadd)
try:
# perform conversion
h5data = cli_convert(path=path_in,
ret_data=True,
profile="test_8440_prof_convert")
cfg = config.ConfigFile(path_out)
assert np.allclose(cfg["meta"]["medium index"], 1.346)
assert np.allclose(cfg["meta"]["pixel size um"], 1.34)
assert np.allclose(cfg["meta"]["wavelength nm"], 554.2)
with qpimage.QPSeries(h5file=h5data, h5mode="r") as qps:
assert np.allclose(qps[0]["medium index"], 1.346)
assert np.allclose(qps[0]["pixel size"], 1.34e-6)
assert np.allclose(qps[0]["wavelength"], 554.2e-9)
except BaseException:
raise
finally:
# cleanup
argsrem = argparse.Namespace(subparser_name="remove",
name="test_8440_prof_convert")
profile.cli_profile(args=argsrem)
def test_iter():
h5file = pathlib.Path(__file__).parent / "data" / "bg_tilt.h5"
qpi = qpimage.QPImage(h5file=h5file, h5mode="r")
series = qpimage.QPSeries(qpimage_list=[qpi, qpi, qpi])
for qpj in series:
assert qpj == qpi
def test_series_meta():
h5file = pathlib.Path(__file__).parent / "data" / "bg_tilt.h5"
try:
qpimage.QPImage(h5file=h5file,
meta_data={"wavelength": 333e-9},
h5mode="r")
except OSError:
# no write intent on file
pass
else:
assert False, "should not be able to write"
qpi0 = qpimage.QPImage(h5file=h5file, h5mode="r")
tf = tempfile.mktemp(suffix=".h5", prefix="qpimage_test_")
tf = pathlib.Path(tf)
with qpi0.copy(h5file=tf):
pass
qpi1 = qpimage.QPImage(h5file=tf,
meta_data={"wavelength": 335e-9})
assert qpi1.meta["wavelength"] == 335e-9
qps = qpimage.QPSeries(qpimage_list=[qpi1], meta_data={
"wavelength": 400e-9})
assert qps.get_qpimage(0).meta["wavelength"] == 400e-9
# cleanup
try:
tf.unlink()
except OSError:
pass
def test_series_error_noqpimage():
try:
qpimage.QPSeries(qpimage_list=["hans", 1])
except ValueError:
pass
else:
assert False, "qpimage list must contain QPImages"
def test_change_wavelength():
_qpi, path, dout = setup_test_data()
path_out = drymass.convert(path_in=path,
dir_out=dout,
meta_data={"wavelength": 500e-9})
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qpso:
id1 = qpso.identifier
path_out2 = drymass.convert(path_in=path,
dir_out=dout,
meta_data={"wavelength": 333e-9})
with qpimage.QPSeries(h5file=path_out2, h5mode="r") as qpso:
id2 = qpso.identifier
assert id1 != id2, "Files should have different identifiers"
def test_series_from_list():
h5file = pathlib.Path(__file__).parent / "data" / "bg_tilt.h5"
qpi1 = qpimage.QPImage(h5file=h5file, h5mode="r")
qpi2 = qpi1.copy()
qps = qpimage.QPSeries(qpimage_list=[qpi1, qpi2])
assert len(qps) == 2
assert qps.get_qpimage(0) == qps.get_qpimage(1)
def test_series_from_h5file():
h5file = pathlib.Path(__file__).parent / "data" / "bg_tilt.h5"
qpi1 = qpimage.QPImage(h5file=h5file, h5mode="r")
qpi2 = qpi1.copy()
tf = tempfile.mktemp(suffix=".h5", prefix="qpimage_test_")
with qpimage.QPSeries(qpimage_list=[qpi1, qpi2], h5file=tf, h5mode="a"):
pass
qps2 = qpimage.QPSeries(h5file=tf, h5mode="r")
assert len(qps2) == 2
assert qps2.get_qpimage(0) == qpi1
# cleanup
try:
os.remove(tf)
except OSError:
pass
def test_series_h5file():
tf = tempfile.mktemp(suffix=".h5", prefix="qpimage_test_")
with h5py.File(tf, mode="a") as fd:
qps = qpimage.QPSeries(h5file=fd)
assert len(qps) == 0
# cleanup
try:
os.remove(tf)
except OSError:
pass
def test_h5file_confusion():
# make up temporary series file
seriesfile = tempfile.mktemp(suffix=".h5", prefix="test_qpimage_series_")
try:
# h5file should be specified with its corresponding parameter
qpimage.QPSeries(seriesfile)
except ValueError:
pass
else:
assert False, "h5file must be given as kwarg!"
def test_bg_corr_index():
_qpi, path_in, path_out = setup_test_data(num=2)
cfg = config.ConfigFile(path_out)
cfg.set_value(section="bg", key="phase data", value=1)
cfg.set_value(section="bg", key="amplitude data", value=1)
h5data = cli_convert(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data, h5mode="r") as qps:
assert np.all(qps[0].pha == 0)
assert np.all(qps[0].amp == 1)
def test_force_roi():
qpi, path_in, path_out = setup_test_data(num=2)
cfg = config.ConfigFile(path_out)
cfg.set_value(section="meta", key="pixel size um", value=1)
cfg.set_value(section="roi", key="force", value=((10, 160), (24, 178)))
h5data = cli_extract_roi(path=path_in, ret_data=True)
with qpimage.QPSeries(h5file=h5data) as qps:
assert qps[0].shape == (150, 154)
assert np.allclose(qpi.pha[10:160, 24:178], qps[0].pha)
assert np.all(qps[0].pha == qps[1].pha)
def test_simple_qpseries():
path = setup_test_data_recursive(n=2, num=3)
ps = dialog.recursive_search(path)
assert len(ps) == 2
# make sure files are the right ones
for ii in range(len(ps)):
with qpimage.QPSeries(h5file=ps[ii], h5mode="r") as qps:
assert len(qps) == 3
def test_basic():
qpi, path, dout = setup_test_data(num=2)
path_out = drymass.analyze_sphere(path, dir_out=dout)
with qpimage.QPSeries(h5file=path_out, h5mode="r") as qpso:
assert qpso[0].shape == qpi.shape
assert qpso[0]["wavelength"] == qpi["wavelength"]
assert qpso[0]["pixel size"] == qpi["pixel size"]
assert qpso[0]["medium index"] == qpi["medium index"]
assert qpso[0]["identifier"].count("projection")
def test_qpseries_with_bad_data():
path = setup_test_data_recursive(n=2, num=3)
(path / "bad_data.h5").write_text("This file should be ignored.")
ps = dialog.recursive_search(path)
assert len(ps) == 2
# make sure files are the right ones
for ii in range(len(ps)):
with qpimage.QPSeries(h5file=ps[ii], h5mode="r") as qps:
assert len(qps) == 3
def is_series_file(path):
"""Return True if `path` is a qpimage.QPSeries file with identifier"""
valid = False
if pathlib.Path(path).exists():
try:
with qpimage.QPSeries(h5file=path, h5mode="r") as qps:
if len(qps) and qps.identifier is not None:
valid = True
except (IOError, OSError):
# corrupt file
pass
return valid
def test_identifier_qpimage():
size = 20
pha = np.repeat(np.linspace(0, 10, size), size)
pha = pha.reshape(size, size)
qpi1 = qpimage.QPImage(data=1.1 * pha, which_data="phase")
qpi2 = qpimage.QPImage(data=1.2 * pha, which_data="phase")
qpi3 = qpimage.QPImage(data=1.3 * pha, which_data="phase")
series = qpimage.QPSeries(qpimage_list=[qpi1, qpi2])
series.add_qpimage(qpi=qpi3, identifier="hastalavista")
assert series[2]["identifier"] == "hastalavista"
def test_series_error_key():
h5file = pathlib.Path(__file__).parent / "data" / "bg_tilt.h5"
qpi1 = qpimage.QPImage(h5file=h5file, h5mode="r")
qpi2 = qpi1.copy()
qps = qpimage.QPSeries(qpimage_list=[qpi1, qpi2])
try:
qps.get_qpimage(2)
except KeyError:
pass
else:
assert False, "get index 2 when length is 2"
